For reduced-order accuracy and control system design of model reduction in active control, the folding wing is taken as an example. The structural dynamic model is established based on the modal synthesis method. Two different reduced order models are obtained by virtue of modal cost analysis and balanced truncation. The comparisons and analyses of two different reduction models rely on degree of controllability and degree of observability. Finally, the optimal control law is applied to the reduction models to restrain the vertical displacement of the wing tip. The results indicate that the degree of controllability of balanced truncation reduction model is higher while the degree of observability of modal cost analysis reduction model is higher. The low order model of structural dynamic model can be achieved using two different reduction methods quickly and precisely. It is effective to design the active control system for the low order model.